.mdl

With apps called 3DMF_OpenGL and Meshwork. Model your model in Meshwork then export it as a 3DMF file. Open up 3DMF_OpenGL and then import the model. Convert and export the model. 3DMF_OpenGL creates .mdl files, plus it is open-source. Meshwork can be found at http://www.codenautics.com/meshwork and 3DMF_OpenGL can be downloaded from http://www.strout.net/files/3DMFOGL.sea.hqx. Hope this helps.

You could use some of id's utilities. They're all DOS programs, but they probably shouldn't be that difficult to port over (I believe they're all simple command line apps...though I haven't looked through the source very much). If that fails, there's always DOS emulators...or PeeCees at work/school, whichever applies to you.

There's also MeQuanno, a Quake-specific model maker, but it requires Meshwork files to do animations and is slightly out-of-date.